openproblems-bio / openproblems

Related projects: ⓘ

• theislab / scarches
  Reference mapping for single-cell genomics
  ☆327Updated 3 weeks ago
• theislab / scib
  Benchmarking analysis of data integration tools
  ☆291Updated 2 weeks ago
• scverse / scanpy-tutorials
  Scanpy Tutorials.
  ☆182Updated this week
• morris-lab / CellOracle
  This is the alpha version of the CellOracle package
  ☆300Updated last week
• aristoteleo / dynamo-release
  Inclusive model of expression dynamics with conventional or metabolic labeling based scRNA-seq / multiomics, vector field reconstruction …
  ☆413Updated last week
• Teichlab / celltypist
  A tool for semi-automatic cell type classification
  ☆279Updated 3 months ago
• agitter / single-cell-pseudotime
  An overview of algorithms for estimating pseudotime in single-cell RNA-seq data
  ☆396Updated 2 weeks ago
• dylkot / cNMF
  Code and example data for running Consensus Non-negative Matrix Factorization on single-cell RNA-Seq data
  ☆261Updated 3 weeks ago
• gao-lab / GLUE
  Graph-linked unified embedding for single-cell multi-omics data integration
  ☆365Updated 6 months ago
• BayraktarLab / cell2location
  Comprehensive mapping of tissue cell architecture via integrated single cell and spatial transcriptomics (cell2location model)
  ☆306Updated 3 weeks ago
• crazyhottommy / awesome_spatial_omics
  tools and notes for spatial omics
  ☆212Updated 5 months ago
• theislab / scvelo
  RNA Velocity generalized through dynamical modeling
  ☆410Updated 2 weeks ago
• broadinstitute / Tangram
  Spatial alignment of single cell transcriptomic data.
  ☆249Updated 3 months ago
• aertslab / pySCENIC
  pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which…
  ☆418Updated 5 months ago
• dynverse / dynbenchmark
  Comparison of methods for trajectory inference on single-cell data 🥇
  ☆191Updated last year
• theislab / cellrank
  CellRank: dynamics from multi-view single-cell data
  ☆342Updated this week
• scverse / scirpy
  A scanpy extension to analyse single-cell TCR and BCR data.
  ☆214Updated this week
• scverse / muon
  muon is a multimodal omics Python framework
  ☆209Updated 2 months ago
• pinellolab / scATAC-benchmarking
  Benchmarking computational single cell ATAC-seq methods
  ☆176Updated 3 years ago
• cellgeni / sceasy
  A package to help convert different single-cell data formats to each other
  ☆370Updated 6 months ago
• saeyslab / nichenetr
  NicheNet: predict active ligand-target links between interacting cells
  ☆467Updated 2 weeks ago
• broadinstitute / CellBender
  CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.
  ☆280Updated 2 months ago
• theislab / diffxpy
  Differential expression analysis for single-cell RNA-seq data.
  ☆191Updated last year
• r3fang / SnapATAC
  Analysis Pipeline for Single Cell ATAC-seq
  ☆301Updated last year
• BiomedicalMachineLearning / stLearn
  A novel machine learning pipeline to analyse spatial transcriptomics data
  ☆189Updated 3 months ago
• mousepixels / sanbomics_scripts
  scripts and notebooks from sanbomics
  ☆339Updated 2 months ago
• scverse / pertpy
  Perturbation Analysis in the scverse ecosystem.
  ☆126Updated this week
• saezlab / liana-py
  LIANA+: an all-in-one framework for cell-cell communication
  ☆153Updated last week
• dmcable / spacexr
  Spatial-eXpression-R: Cell type identification (including cell type mixtures) and cell type-specific differential expression for spatial …
  ☆292Updated 3 months ago
• ventolab / CellphoneDB
  CellPhoneDB can be used to search for a particular ligand/receptor, or interrogate your own HUMAN single-cell transcriptomics data.
  ☆317Updated 2 months ago